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Multiprocessing and running jobs on server using slurm

Category: 
Structure prediction
PyRosetta

I have a question regarding parallelizing some of the bash scripts from the refinement and denovo prediction tutorials. They usually rely on GNU parallel to run across many cores, substituting some variable in the script with a number from the GNU parallel run command . I wonder how I can run the same scripts on a server running slurm workload manager, or any other possible multiprocessing strategy using Python.

Post Situation: 

cleanATOM() for non-ideal amino acids

Category: 
PyRosetta

Hello People,

 

I am trying to clean this protein 3HZ7.pdb using pyrosetta.toolbox.cleaning.cleanATOM('3HZ7.pdb') in order to use it within PyRosetta.

The protein has MSE (Selenomethionine?) instead of MET at different parts of the sequence, therefore when applying cleanATOM() it just deletes these amino acids and I end up with a broken backbone (attached figure).

 

Post Situation: 

Output several poses in a silent file

Category: 
PyRosetta

Hi,

If I have a list of poses, how can I go about writing a single silent file that contains these poses?  I see there's a SilentFilePoseInputStream class, but I can't find a way to output in silent format.  Can someone point me to those functions?

 

Thanks in advance.

Post Situation: 

PyRosetta compiled with GLIBC 2.12

Category: 
Compilation
PyRosetta

Hello,

We are trying to install PyRosetta on CentOS 6.  The current compilation of PyRosetta (PyRosetta4.Release.python27.linux.release-171.tar.bz2) requires GLIBC_2.14.

However, our system's GLIBC version is 2.12 and the compilation of PyRosetta stop with the error

                          ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cm/shared/apps/pyrosetta/python/2.7/4.171/lib/python2.7/site-packages/pyrosetta-2018.9+release.333d996-py2.7-linux-x86_64.egg/pyrosetta/rosetta.so)

Post Situation: 

Sample dihedral database

Category: 
PyRosetta

Good morning,

 

I have a database of dihedral angles in this order: residue psi psi. Is is possible to use pyrosetta to sample randomly throuh this database,

applying random psi and psi angles to a pdb pose, using a movemap? Imagine that my sequence is AQAAVFGT; so the script would retrieve randomly from the database the dihedrals corresponding to residues in the sequence and output a pose.

is this possible? Maybe with a loop with the SetTorsion mover?

Thank you,

cheers

Post Situation: 

generate_nonstandard_residue_set() takes exactly 2 arguments (1given)

Category: 
PyRosetta

So I'm trying to load this ligand_protein complex PDB into PyRosetta by temporarily creating a ResidueTypeSet

from pyrosetta import *

init()

params_path = Vector1(['cefotaxime.params', 'cefotaxime.params'])

nonstandard_residue_type = generate_nonstandard_residue_set(params_path)

I got this error message:

 

generate_nonstandard_residue_set() takes exactly 2 arguments (1given)

 

Post Situation: 

What is the expected behaviour when minimizing a jump edge?

Category: 
Docking
Constraints
PyRosetta

I have seen references to minimization of a jump edge (e.g using a MinMover object) leading to both rotations and translations downstream of the jump. 

I am modelling an interaction between two proteins, connected in the fold tree by a single jump edge, with atom pair constraints defined to bring them into close proximity.

I allow movement of this jump in the movemap (set_jump), atom_pair_constraints is activated in the scorefunction, and the fold tree is valid.  

Post Situation: 

Passing a dictionary from pyrosetta to rosetta

Category: 
PyRosetta

Hi,

I'd like to create a function in rosetta (in C++) that ultimately will accept a python dictionary when called from pyrosetta.  What's the best C++ class to use that will be the easiest for me to do the conversion from python dict?  (i.e. is there any existing pyrosetta code that will convert a python dictionary to, say, a C++ map).

Thanks in advance.

Post Situation: 

Import error undefined symbol and Anaconda python

Category: 
PyRosetta

I have a few questions regarding Pyrosetta 4:

First I have Anaconda2 which comes with python installed at /home/MYUSERNAME/anaconda2/bin/python, however the installation uses the default python at /usr/bin/python and its site packages directory in  /usr/lib/python2.7/site-packages.

1) How can I uninstall pyrosetta?

2) How can I install it for the Anaconda python?

 

Second, running native python, trying >>> from rosetta import * gives:

Post Situation: 

Using ref2015 and talaris2014 in the same script

Category: 
PyRosetta

Hi,

I'm using pyrosetta compiled from rosetta_src_2017.39.  I was wondering whether it's possible to use both talaris2014 and ref2015 in the same script.  When I try to set up a scoring function using talaris2014 weights, I get this error:

pyrosetta.create_score_function("talaris2014")

ERROR: talaris2014(.wts) requested, but -corrections::restore_talaris_behavior not set to true. This leads to a garbage scorefunction.  Exiting.

 

Post Situation: 

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